AIM To determine the prevalence of Chlamydia trachomatis(CT)and Neisseria gonorrhea(GC)in young men seeking care in the emergency department(ED)for non-sexually transmitted infection(STI)related symptoms.METHODS This was a prospective,cross-sectional study in an urban ED.The main outcome was the rate of positive CT and GC on urine nucleic acid amplification testing in males aged 16-21 presenting with non-STI related complaints.RESULTS Two hundred and eighty-four patients were enrolled,271 were included in the final data analysis[age range 16-21,median:18(quartiles 16-18,19-21)].Overall,17(6.3%,95%CI:4%-10%)tested positive for CT and 0%(95%CI:0%-2%)were found to have GC.The proportion of sexually active subjects was 71%(95%CI:65%-76%)and 2%(95%CI:0.6%-4%)reported sex with men.Previous STI testing was reported in 46%(95%CI:43%-54%)and 13%(95%CI:8%-20%)of those patients previously tested had a history of STI.Of the patients who tested positive for CT in the ED,88%(95%CI:64%-98%)were successfully followed up.CONCLUSION The prevalence of CT infection found by screening was 6.3%.Screening and follow-up from the ED was successful.The findings justify routine STI screening in male adolescents presenting to the ED with non-STI related complaints.